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Sample GSM1904422 Query DataSets for GSM1904422
Status Public on May 12, 2016
Title RNA-Seq_MGG8_KD [Sample 6]
Sample type SRA
 
Source name MGH8 Glioma stem-like cells
Organism Homo sapiens
Characteristics cell line: MGG8
cell type: Glioma cell line
cell subtype: Cancer stem-like cells
infected with: shRNA sequence targeting Imp2
genotype/variation: IMP2 knockdown
Treatment protocol MGH8 cell line infected with shRNA sequence targeting Imp2
Growth protocol Neurobasal medium (Invitrogen) supplemented with L-glutamine (Glutamax, Gibco), B27 supplement (Invitrogen), N2 supplement (Invitrogen), 20 ng/mL recombinant human EGF (R&D Systems), 20 ng/ml recombinant human FGF2 (R&D Systems). Puromycin selection for 5 days
Extracted molecule polyA RNA
Extraction protocol Total RNA extraction kit Exiqon, on colum DNASE treatment (Qiagen)
Illumina polyA stranded
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description processed data: RNA_IMP2s_KD.txt
Data processing Genomic alignment with TopHat 2.0.12, --b2-very-sensitive --library-type fr-firststrand --b2-N 1
Differential expression calling with edgeR 3.10.2 and R 3.2.0
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited textfile containing the raw readcounts, normalized cpm and gene fold-changes
 
Submission date Oct 08, 2015
Last update date May 15, 2019
Contact name Tommy Beat Schlumpf
Organization name ETH Z├╝rich
Department D-BSSE
Lab Paro
Street address Mattenstrasse 26
City Basel
State/province Basel-Stadt
ZIP/Postal code 4058
Country Switzerland
 
Platform ID GPL18573
Series (2)
GSE73845 Functional characterization of RNA-binding protein IMP2 in primary Glioma cell lines [HTS]
GSE73847 Functional characterization of RNA-binding protein IMP2 in primary Glioma cell lines
Relations
BioSample SAMN04156653
SRA SRX1317320

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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